## [1] "O76_p4_con_R1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
83,976,768 |
83,976,768 |
| Not Truncated |
49,754,625 |
47,242,494 |
| Truncated |
34,222,143 |
36,734,274 |
Truncated Read Length
| Average Length Truncated |
47.6 |
47.9 |
Mapping Efficiency
| Too Short To Map |
4,735,654 |
4,722,713 |
| Unique Alignments |
72,611,776 |
70,587,608 |
| Multiple Alignments |
2,684,238 |
2,819,963 |
| Failed To Align |
3,945,100 |
5,846,484 |
| Paired |
61,860,138 |
61,860,138 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
34,589,649 |
| Invalid Pairs |
27,270,489 |
| Same Circularised |
103,129 |
| Same Dangling Ends |
2,747,237 |
| Same Fragment Internal |
11,321,757 |
| Re Ligation |
8,896,972 |
| Contiguous Sequence |
416,123 |
| Wrong Size |
3,785,271 |
| Total Pairs |
61,860,138 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
34,589,649 |
45,717 |
| Cis-close (<10Kbp) |
5,924,917 |
5,559 |
| Cis-far (>10Kbp) |
21,296,797 |
24,789 |
| Trans |
7,367,935 |
15,369 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
